From 50a44d037bb86703f405c5903ffa944222ce0052 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 9 Apr 2020 17:02:36 +0200
Subject: [PATCH] better docs and organisation of giles

---
 README.md                               | 12 ++++++++++--
 conf/pipeline/viralrecon/genomes.config | 16 ++++++++++++++++
 docs/pipeline/viralrecon/genomes.md     |  9 +++++++++
 pipeline/viralrecon.config              | 11 +----------
 4 files changed, 36 insertions(+), 12 deletions(-)
 create mode 100644 conf/pipeline/viralrecon/genomes.config
 create mode 100644 docs/pipeline/viralrecon/genomes.md

diff --git a/README.md b/README.md
index 49283ed..17ce78c 100644
--- a/README.md
+++ b/README.md
@@ -15,6 +15,7 @@ A repository for hosting Nextflow configuration files containing custom paramete
   * [Documentation](#documentation)
   * [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
 * [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
+  * [Pipeline-specific institutional documentation](#pipeline-specific-institutional-documentation)
   * [Pipeline-specific documentation](#pipeline-specific-documentation)
   * [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
   * [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
@@ -159,9 +160,9 @@ Each configuration file will add new params and overwrite the params already exi
 
 Note that pipeline-specific configs are not required and should only be added if needed.
 
-### Pipeline-specific documentation
+### Pipeline-specific institutional documentation
 
-Currently documentation is available for the following pipeline within the specific profile:
+Currently documentation is available for the following pipelines within specific profiles:
 
 * ampliseq
   * [BINAC](docs/pipeline/ampliseq/binac.md)
@@ -174,6 +175,13 @@ Currently documentation is available for the following pipeline within the speci
   * [MUNIN](docs/pipeline/sarek/munin.md)
   * [UPPMAX](docs/pipeline/sarek/uppmax.md)
 
+### Pipeline-specific documentation
+
+Currently documentation is available for the following pipeline:
+
+* viralrecon
+  * [genomes](docs/pipeline/viralrecon/genomes.md)
+
 ### Enabling pipeline-specific configs within a pipeline
 
 :warning: **This has to be done on a fork of the `nf-core/<PIPELINE>` repository.**
diff --git a/conf/pipeline/viralrecon/genomes.config b/conf/pipeline/viralrecon/genomes.config
new file mode 100644
index 0000000..45c8247
--- /dev/null
+++ b/conf/pipeline/viralrecon/genomes.config
@@ -0,0 +1,16 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/viralrecon custom profile Nextflow config file
+ * -------------------------------------------------
+ * Defines viral reference genomes for all environments.
+ */
+ 
+params {
+  // Genome reference file paths
+  genomes {
+    'NC_045512.2' {
+      fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/NC_045512.2.fasta.gz"
+      gff   = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/NC_045512.2.gff.gz"
+    }
+  }
+}
diff --git a/docs/pipeline/viralrecon/genomes.md b/docs/pipeline/viralrecon/genomes.md
new file mode 100644
index 0000000..9577434
--- /dev/null
+++ b/docs/pipeline/viralrecon/genomes.md
@@ -0,0 +1,9 @@
+# nf-core/configs: viralrecon specific configuration
+
+Extra specific configuration for viralrecon pipeline
+
+## Usage
+
+Will be used automatically when running the pipeline with the shared configs in the nf-core/configs repository
+
+This will download and launch the viralrecon specific [`viralrecon.config`](../../../conf/pipeline/viralrecon/genomes.config) which has been pre-configured with custom genomes.
diff --git a/pipeline/viralrecon.config b/pipeline/viralrecon.config
index 45c8247..25d93c4 100644
--- a/pipeline/viralrecon.config
+++ b/pipeline/viralrecon.config
@@ -2,15 +2,6 @@
  * -------------------------------------------------
  *  nfcore/viralrecon custom profile Nextflow config file
  * -------------------------------------------------
- * Defines viral reference genomes for all environments.
  */
  
-params {
-  // Genome reference file paths
-  genomes {
-    'NC_045512.2' {
-      fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/NC_045512.2.fasta.gz"
-      gff   = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/NC_045512.2.gff.gz"
-    }
-  }
-}
+includeConfig "${params.custom_config_base}/conf/pipeline/viralrecon/genomes.config" }
\ No newline at end of file